Programming by Optimization

Posted on April 5, 2012 by | 2 comments

In today’s increasingly computer-oriented world, the development of software must also keep up with achieving certain tasks to meet demands. During the creation of such software, however, developers often explore different methods or paths in order to achieve a desired task. A problem that often arises though is that during the development of this “desired task”, alternate solutions that are thought to be nearly impossible to use gets thrown away, when in reality these methods might have worked later on.

Fortunately, Dr. Holger Hoos along with his research team at the University of British Columbia are working on introducing a type of design called Programming by Optimization (PbO) that directly prevents this premature toss of solutions. This has been proved to be incredibly beneficial to the development of software and leads to huge increases in software efficiency.

This is excellent news for the computer world as one of the biggest goals of large companies is increasing processing speeds and reducing running costs by, for example, using better organizational and scheduling procedures. This is where PbO shines!

PbO allows users to locate mistakes that weren’t noticed at first – this is the debugging process. PbO debugs all problems of each step in creating software separately by using interchangeable codes and provides a more efficient way of finding the correct problem. Dr. Hoos and his research team have already found a bug in a widely used commercial software using PbO and the company expressed their gratitude for it.

Although PbO is still in the research process, it has gathered a lot of attention from major companies around the world. Among others, Google showed great interest in PbO and the research team is currently working with IBM as well.

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A component of PbO that makes it so amazing and attractive to companies is its flexibility and adaptability to software and data centers. The video above mentioned university exam timetabling as an example. Since exam periods involve many students and courses, it is very difficult to put together exam times that fit every student’s schedule. This is complicated further with the limited number of rooms available during an exam period that only lasts a couple weeks.

Now, if we were to compare the Spring semester to say, the Summer semester, you can imagine that each semester will have entirely new courses. With PbO, the scheduling of these diverse timetables comes at ease. This also works across universities, so optimization can generalize the different situations so that it can be applied to scheduling at UBC Vancouver as well as UBC Okanagan.

Data center. Image by The Ark.

The following podcast is a short talk by Dr. Hoos explaining how PbO can help data centers run better:

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As more and more software get developed, programmers need a general plan to guide them through the designing process, so we can all continue to benefit from the efficiency and creativity that optimized software bring to us everyday.

References & further reading:

Hoos, H. 2012. Programming by Optimization. Magazine Communications of the ACM, 55(2). http://cacm.acm.org/magazines/2012/2/145402-programming-by-optimization/fulltext

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Could the new Cyclosporin be in our own bodies?

Posted on April 5, 2012 by | Leave a comment

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The Immune system Simplified (Nobel Media)

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Recent research at the BC children’s hospital in Vancouver, Canada has unearthed one of the mysteries of an immune cell that may play a key role in combating auto-immune diseases.

"A Regulatory T Cell" Image Source: http://www.iayork.com/Images/2008/12-8-08/BioLegendTReg.png

The cell in question is the regulatory T cell (Treg), a regulatory cell responsible for the management of immune responses. While largely unstudied, this cell has been found to prevent disease and illness brought on by the body’s own immune system. Tregs monitor our immune systems and counter-balance the constant assault against the cells within our bodies both malignant and benign. In a sense, they’re the whistle blowers of the body police.

While the job of Tregs is to control and reduce immune response, they can also be used to quell a person’s runaway immune system and subdue the illnesses our immune systems can sometimes create.

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While Treg therapy may seem futuristically out of reach or too good to be true, preliminary trials so far demonstrated promising results in human and mouse models. Anti-immune therapies using Tregs have been so effective and versatile that they not only treat the inflammation in Crohn’s Disease but tissue rejection in organ transplants. At times, this cell is  even capable of giving the body life long tolerance to the transplanted foreign organs.

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"Simplified Illustration of the Inflammatory Response" Image Source: http://www.rkm.com.au/immunology/immune-images/IMMUNE-inflammation-R-600.jpg

Despite these triumphs, Treg therapies still have a long way to go. The recent discovery found by the BC researchers shed light on interactions of Tregs with Neutrophils, immune cells involved in the generic first response of immune systems. While Tregs are meant to suppress immune responses, they seem to attract neutrophils in vast quantities which are highly inflammatory in nature. Until more is known about the relationships and functions of Tregs, researchers may run the risk of accidentally triggering an immune response when trying to reduce it. Another possible risk to consider is that Treg therapy may increase our risk of cancer by suppressing the cells responsible for keeping it in check.

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Despite these risks it is obvious that Treg therapies have an untapped potential with almost limitless application to illnesses associated with an overactive immune system. Our bodies’ tolerance of Tregs and their adaptive and responsive nature make them not only ideal in that they act like living cyclosporine, but they have been tweaked and perfected to be the ideal  immune suppressant for over millennia, before we ever got sick.

 

 

 

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The Haber process

Posted on April 4, 2012 by | Leave a comment

The Haber process is the nitrogen fixation reaction of nitrogen gas and hydrogen gas using an iron or ruthenium catalyst, under high temperature of 500c and pressure of 250 atmospheres (Clark 2002). The goal of the process is to convert nitrogen and hydrogen from the atmosphere to ammonia (NH3). Ammonia is very important to fertilizer industry.  Approximately 80% of ammonia is used as fertilizers and it helps provide increased yield of crops (Clark 2002). One of the top challenges for organometallic chemistry is to find a way to catalytically produce ammonia from nitrogen at room temperature and ambient pressure.

Although nitrogen gas makes up 78% of Earth’s atmosphere, it is chemically unreactive under normal condition due to the triple bond between two nitrogen atoms. High energy is needed to break these bonds (Ausetute 2012). Nitrogen fixation occurring in plants is slow. With the help of the Haber process, nearly 100 million tons of ammonia fertilizer is produced every year, yielding taller and healthier crops.

N2 (g) + 3 H2 (g) ⇌ 2 NH3 (g)   (ΔH = −92.22 kJ*mol−1)

The production of ammonia is exothermic. There are 4 molecules on the left-hand side and only 2 on the right-hand side. The reaction is reversible and will reach equilibrium when the rate of forward reaction equals the rate of reverse reaction.

If we increase the pressure the system will favour the reaction, producing more ammonia. This is Le Chatelier’s Principle. To get more ammonia produced, high pressure, i.e. 250 atmospheres is needed. Increasing the pressure also speeds the reaction. Under high pressure, molecules are brought closely together and able to contact with the surface of the catalyst. The higher the pressure, the faster the rate of a gas reaction will be.

The catalyst, on the other hand, does not play a role in the position of chemical equilibrium. It lowers activation energy and hence increases the reaction rate. Osmium and ruthenium were used as catalysts at first and iron catalyst is used more often now (Ausetute 2012). Iron is more active so less pressure is needed.

In UBC, Dr. Martinez and her research group are trying to find a way to obtain hydrogen and nitrogen from air and make ammonia without consuming too much energy.

Our video, discussing nitrogen, ammonia, the Haber process and its impact on the fertilizer industry.

https://www.youtube.com/watch?v=T6S02rwVUp8&feature=player_embedded

Our podcast. A brief overview of the environmental impact of the use and production of  nitrogen fertilizers.

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References:

Clark,J. 2002. http://www.chemguide.co.uk/physical/equilibria/haber.html (accessed Apr.  1 2012)

Asecute. 2012. http://www.ausetute.com.au/haberpro.html (accessed Apr. 1 2012)

Pictures:

http://www.nasdaqinsurance.com/wp-content/uploads/2011/07/crops-insurance.jpg

 

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Why do we have acne?

Posted on March 22, 2012 by | 2 comments

Acne is a technically a type of human skin disease. This includes whiteheads, blackheads and inflamed area of skin.

Why do we have acne?

The formation of acne is mainly because the pore of the skin is clogged. Each pore contains a sebaceous gland and this gland makes sebum which is oil that lubricates our hair and skin. A sebaceous gland usually functions normally and produces right amount of sebum in the pore. However, since teenager’s body starts to develop, hormones stimulate the sebaceous gland to make more sebum. When there is too much oil inside the pore, it will be clogged. Bacteria called Propionibacterium acnes can be easily trapped inside the pore. Swelling and redness symbolizes the start of acne.


 I am no longer a teen.

We are not teens but why do we still have acne? Acne is also triggered by hormonal changes due to stress, menstrual periods and pregnancy (Palmer 2010). Acne certainly affects people of all ages.

What should we do if we have acne?

There are three things that we should do. We should clean our skin gently, try not to touch our skin, and see a dermatologist if acne becomes worse. Dermatologists suggest that we should not pop or squeeze acne, although it is very tempting to do (Palmer 2010). Popping acne increases a chance of making it worse (MedlinePlus 2011). This irritation of the skin may cause permanent acne scars which are harder to get rid of (AcneNet 2010).

This video tells us why it is bad to pop acne in detail.

Popping-Pimples.htm

Palmer,A. 2010. Diagosing Acne. http://acne.about.com/od/diagnosisofacne/a/diagnosis.htm (accessed 3/21/2012)

MedlinePlus. 2011. Acne. http://www.nlm.nih.gov/medlineplus/acne.html (accessed 3/21/2012)

AcneNet. 2010. What causes Acne? http://www.skincarephysicians.com/acnenet/acne.html (accessed 3/21/2012)

Wikipedia. 2012. Propionibacterium acnes. http://en.wikipedia.org/wiki/Propionibacterium_acnes (accessed 3/21/2012)

Wikipedia. 2012. Sebaceous gland. http://en.wikipedia.org/wiki/Sebacious_gland (accessed 3/21/2012)

Video:

http://video.about.com/acne/Popping-Pimples.htm

Picture:

http://www.nlm.nih.gov/medlineplus/images/acne.jpg

http://www.nlm.nih.gov/medlineplus/ency/images/ency/fullsize/19666.jpg

 

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When Your Genes Trick You

Posted on March 17, 2012 by | Leave a comment

Our body is governed by our genes. Our genes specify what type of proteins should be produced by our cells, and proteins are responsible for almost everything in our body. Each protein has three dimensional shape; proteins’ shape indicate their job in the body.

DNA has the information to to make proteins, and proteins are responsible for almost everything in our body ( from : http://www.flyfishingdevon.co.uk/salmon/year3/psy339evaluation-evolutionary-psychology/evaluation-evolutionary-psychology.htm )

In this blog I would like to talk about a genetic condition, called Thalassemia which so many  people in the world have it and simply are not aware of it. In people with Thalassemia, the shape of their hemoglobin protein in some of  their red blood cells is different because in their body the genes that have the information for hemoglobin production have been altered. Therefore, since shape of a protein specifies its functionality, hemoglobin becomes inefficient in transferring oxygen.(http://www.cdc.gov/Features/Thalassemia/)

shape some of the red blood cells in people with Thalassemia is oval or sickle shape( from :http://www.islamicboard.com/health-science/134270536-medical-student-review-2.html )

Thalassemia has two version of minor and major. Thalassemia minor in most cases does show significant signs or symptoms, that is why so many people may have it and are not aware of it. However people with major Thalassemia require advanced medical care and mostly they do not live very long.( http://www.medicinenet.com/beta_thalassemia/article.htm )

According to Dr. Greenberg this condition is often mistaken by iron deficiency in the nutrition. The reason is that  hemoglobin in people with Thalassemia is not capable of utilizing enough iron because of its faulty protein structure, as a result, their  blood tests show lower amount of iron compared to normal range. Misdiagnosis of Thalassemia and consumption of iron pills in fact accumulates in the liver because the iron is not being utilized by hemoglobin and causes damage to people who have Thalassemia and not iron deficiency. link to his article is here >>http://www.utoronto.ca/kids/Thalassemia.htm

Epidemiology and History: Thalassemia is common in discrete regions of the world where malaria was prevalent, such as Asia, Africa, middle-east, and parts of Europe. It is interesting to note that people with such condition could survive malaria at a higher rate than people who did not have Thalassemia. Therefore Thalassemia condition caused a selective survival advantage for carriers(Wikipedia :http://en.wikipedia.org/wiki/Thalassemia ).

Hence, if you are from the countries that Thalassemia is common or your background is from countries mentioned above and your family doctor diagnosed you with either iron deficiency or “anemia” make sure you ask for a genetic test and make sure you do not have Thalassemia.

According to Wikipedia “This genetic disorder is autosomal recessive trait, meaning a person needs to inherit two copies of the gene from each parent for the trait to be expressed. Therefore both parents have to be carriers of a recessive trait in order for a child to express that trait. If both parents are carriers, there is a 25% chance with each child to show the recessive trait”. This is important for people who are carriers of Thalassemia and plan to have kids and become pregnant to make sure their partner is not a carrier.

Here is a link which you can share with your friends to make them awareYouTube Preview Image

 

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Let’s Play Some Mario!!!

Posted on March 14, 2012 by | 2 comments

Do not think Mario games are easy because it is old and many kids are playing it. Mario is actually difficult. You think other people have no problem playing it? You are wrong.

NP-hard (non-deterministic polynomial-time hard) means problems that are at least as hard as the hardest problems in NP. Mario and and many games such as Zelda, Pokemon, and  are considerred as NP-hard. It meas it can be very hard for a player. Here are some examples of Pokemon and Zelda problems.

According to Jacob Aron. Each game can be transformed into a logical puzzle called Boolean satisfiability problem. It is used to determine if variables of a given Boolean  formula can be assigned in such a way as to make the formula evaluate to TRUE. For the games, elements suchs as enemies and mushrooms are assigned as variables in formulas to deteremine if they allow a game level to complete and produce true or make a game level impossible and produce false. In the result, games like Super Mario Bro. are proven to be NP-hard.

Mario games are also NP-complete. Many difficult problems can be classified into the NP-complete catogory. For examples, Salesman and knapsack problems are NP-complete; they require of finding the shortest route between series of points, and  how to allocate resources.

Here is just an example of very hard Mario game. (video contains coarse language. Viewer discreption is advised)

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It is not common to run into Goomba or not be able to jump over the bottomless pit. Since Mario is proven to be a very hard game, dont feel bad to see “GAME OVER” many times.

Reference

1. NewScientist. Jacob Aron. Mario is hard, and that’s mathematically official. [Accessed March 14, 2012. ]

2. Kotaku.  Luke Plunkett. Science Proves Old Video Games Were Super Hard. [Accessed March 14, 2012. ]

2. Wikipedia. [Accessed March 14, 2012. ]

 

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Cutting out the middleman

Posted on March 14, 2012 by | 2 comments

Fungal infection of the bone marrow. Image by euthman.

Nowadays, clinical transplantation is known to save many lives, but not without a catch. Patients have to go through immunosuppressive therapy if the MHC molecules on the graft, or transplanted tissue, do not match their own.

Our bodies are very picky and sensitive. For instance, we are okay with accepting skin grafts from ourselves – this is a type of autograft. However, if we were to be given a skin graft from someone unrelated, this arrangement is not long-lived. We let this allograft stick around for a bit, but ultimately kick it out after 10-13 days. We’ll remember it, too. Like a woman scorned, if this same offensive graft comes again, we boot it out even faster. The T cells living in our bodies as defenders do not take kindly to foreign tissue. Immune responses are mounted as a result, causing transplant rejection. Learn more about the immune response here:

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For clinical transplantation to be successful, people have relied on immunosuppressive drugs to inhibit the defensive mechanisms our cells carry out when we encounter foreign molecules. This is problematic because now people are more susceptible to cancer and infections. The issue with transplant rejection is that donor and recipient cells don’t like each other. What do we do when two people don’t get along? We force them to.

Scientists have recently tested a method for transplant recipients to accept mismatched donor organs. In this ongoing trial, patients are exposed to chemotherapy and radiation and injected with enriched donor stem cells, hoping to achieve what is called “chimeric tolerance”. The idea is to make two immune systems work in one body by destroying the host’s first.

This new approach is pretty questionable. Small sample size aside, it is not known whether the enriched cells really made an impact as the study is missing a control group (where patients would presumably undergo treatment without these cells). Furthermore, these cells were not described very clearly. Suppressing the immune system with chemotherapy and radiation is also unnecessarily harmful and risky. Will it be worth it in the end?

The lengths we will go to in order to cure disease (Image from xkcd.com - click to enlarge).

References:

1. Murphy, Kenneth P. Janeway’s Immunology (8th ed), p652-664.
2. Steenhuysen, Julie. Immune system tricked to accept donor organs: study. NewsDaily. Accessed March 14, 2012.
3. Garland Science. The Immune Response. Youtube video, accessed March 14, 2012.

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Posted in Biological Sciences, Issues in Science, New and innovative science, Science Communication, Science in the News

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